@jbrowse/plugin-comparative-adapters 2.16.1 → 2.18.0

package/dist/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -0,0 +1,66 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
+interface BlastColumns {
+    qseqid?: string;
+    qgi?: string;
+    qacc?: string;
+    sseqid?: string;
+    sallseqid?: string;
+    sgi?: string;
+    sallgi?: string;
+    sacc?: string;
+    sallacc?: string;
+    qstart?: number;
+    qend?: number;
+    sstart?: number;
+    send?: number;
+    qseq?: string;
+    sseq?: string;
+    evalue?: string;
+    bitscore?: string;
+    score?: string;
+    length?: string;
+    pident?: string;
+    nident?: string;
+    mismatch?: string;
+    positive?: string;
+    gapopen?: string;
+    gaps?: string;
+    ppos?: string;
+    frames?: string;
+    qframe?: string;
+    sframe?: string;
+    btop?: string;
+    staxids?: string;
+    sscinames?: string;
+    scomnames?: string;
+    sblastnames?: string;
+    sskingdoms?: string;
+    stitle?: string;
+    salltitles?: string;
+    sstrand?: string;
+    qcovs?: string;
+    qcovhsp?: string;
+    qcovus?: string;
+}
+interface BlastRecord extends BlastColumns {
+    qseqid: string;
+    sseqid: string;
+    qstart: number;
+    qend: number;
+    sstart: number;
+    send: number;
+}
+export default class BlastTabularAdapter extends BaseFeatureDataAdapter {
+    private data;
+    static capabilities: string[];
+    getData(opts?: BaseOptions): Promise<BlastRecord[]>;
+    setup(opts?: BaseOptions): Promise<BlastRecord[]>;
+    hasDataForRefName(): Promise<boolean>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -0,0 +1,200 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
+const util_2 = require("../util");
+function createBlastLineParser(columns) {
+    const columnNames = columns.trim().split(' ');
+    const qseqidIndex = columnNames.indexOf('qseqid');
+    if (qseqidIndex === -1) {
+        throw new Error('Missing required column "qseqid"');
+    }
+    const sseqidIndex = columnNames.indexOf('sseqid');
+    if (sseqidIndex === -1) {
+        throw new Error('Missing required column "sseqid"');
+    }
+    const qstartIndex = columnNames.indexOf('qstart');
+    if (qstartIndex === -1) {
+        throw new Error('Missing required column "qstart"');
+    }
+    const qendIndex = columnNames.indexOf('qend');
+    if (qendIndex === -1) {
+        throw new Error('Missing required column "qend"');
+    }
+    const sstartIndex = columnNames.indexOf('sstart');
+    if (sstartIndex === -1) {
+        throw new Error('Missing required column "sstart"');
+    }
+    const sendIndex = columnNames.indexOf('send');
+    if (sendIndex === -1) {
+        throw new Error('Missing required column "send"');
+    }
+    const columnNameSet = new Map(columnNames
+        .map((c, idx) => [c, idx])
+        .filter(f => !['qseqid', 'sseqid', 'qstart', 'qend', 'sstart', 'send'].includes(f[0])));
+    return (line) => {
+        if (line.startsWith('#')) {
+            return;
+        }
+        const row = line.split('\t');
+        const qseqid = row[qseqidIndex];
+        const sseqid = row[sseqidIndex];
+        const qstart = row[qstartIndex];
+        const qend = row[qendIndex];
+        const sstart = row[sstartIndex];
+        const send = row[sendIndex];
+        if (!(qseqid && sseqid && qstart && qend && sstart && send)) {
+            console.warn('Invalid BLAST line');
+            console.warn(line);
+            return;
+        }
+        const record = {
+            qseqid,
+            sseqid,
+            qstart: Number.parseInt(qstart),
+            qend: Number.parseInt(qend),
+            sstart: Number.parseInt(sstart),
+            send: Number.parseInt(send),
+        };
+        for (const [columnName, idx] of columnNameSet.entries()) {
+            const value = row[idx];
+            if (!value) {
+                continue;
+            }
+            record[columnName] = value;
+        }
+        return record;
+    };
+}
+class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    getData(opts) {
+        if (!this.data) {
+            this.data = this.setup(opts).catch((e) => {
+                this.data = undefined;
+                throw e;
+            });
+        }
+        return this.data;
+    }
+    async setup(opts) {
+        const pm = this.pluginManager;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'blastTableLocation'), pm), opts);
+        const columns = (0, configuration_1.readConfObject)(this.config, 'columns');
+        return (0, util_2.parseLineByLine)(buf, createBlastLineParser(columns));
+    }
+    async hasDataForRefName() {
+        return true;
+    }
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        if (assemblyNames.length === 0) {
+            const query = this.getConf('queryAssembly');
+            const target = this.getConf('targetAssembly');
+            return [query, target];
+        }
+        return assemblyNames;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const feats = await this.getData(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                set.add(idx === 0 ? feat.qseqid : feat.sseqid);
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const blastRecords = await this.getData(opts);
+            const [queryAssembly, targetAssembly] = this.getAssemblyNames();
+            const { refName: queryRefName, assemblyName: queryAssemblyName, start: queryStart, end: queryEnd, } = query;
+            if (queryAssemblyName !== targetAssembly &&
+                queryAssemblyName !== queryAssembly) {
+                console.warn(`${queryAssemblyName} not found in this adapter`);
+                observer.complete();
+                return;
+            }
+            for (let i = 0; i < blastRecords.length; i++) {
+                const r = blastRecords[i];
+                let start;
+                let end;
+                let refName;
+                let assemblyName;
+                let mateStart;
+                let mateEnd;
+                let mateRefName;
+                let mateAssemblyName;
+                const { qseqid, sseqid, qstart, qend, sstart, send, ...rest } = r;
+                if (queryAssemblyName === queryAssembly) {
+                    start = qstart;
+                    end = qend;
+                    refName = qseqid;
+                    assemblyName = queryAssembly;
+                    mateStart = sstart;
+                    mateEnd = send;
+                    mateRefName = sseqid;
+                    mateAssemblyName = targetAssembly;
+                }
+                else {
+                    start = sstart;
+                    end = send;
+                    refName = sseqid;
+                    assemblyName = targetAssembly;
+                    mateStart = qstart;
+                    mateEnd = qend;
+                    mateRefName = qseqid;
+                    mateAssemblyName = queryAssembly;
+                }
+                let strand = 1;
+                let mateStrand = 1;
+                if (start > end) {
+                    ;
+                    [start, end] = [end, start];
+                    strand = -1;
+                }
+                if (mateStart > mateEnd) {
+                    ;
+                    [mateStart, mateEnd] = [mateEnd, mateStart];
+                    mateStrand = -1;
+                }
+                if (refName === queryRefName &&
+                    (0, util_1.doesIntersect2)(queryStart, queryEnd, start, end)) {
+                    observer.next(new SyntenyFeature_1.default({
+                        uniqueId: i + queryAssemblyName,
+                        assemblyName,
+                        start,
+                        end,
+                        type: 'match',
+                        refName,
+                        strand: strand * mateStrand,
+                        syntenyId: i,
+                        ...rest,
+                        mate: {
+                            start: mateStart,
+                            end: mateEnd,
+                            refName: mateRefName,
+                            assemblyName: mateAssemblyName,
+                        },
+                    }));
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}
+BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
+exports.default = BlastTabularAdapter;

package/dist/BlastTabularAdapter/configSchema.d.ts

@@ -0,0 +1,30 @@
+declare const BlastTabularAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    targetAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    queryAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    blastTableLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    columns: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BlastTabularAdapter;

package/dist/BlastTabularAdapter/configSchema.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+function x() { }
+const BlastTabularAdapter = (0, configuration_1.ConfigurationSchema)('BlastTabularAdapter', {
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Query assembly is the first value in the array, target assembly is the second',
+    },
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the target assembly',
+    },
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the query assembly',
+    },
+    blastTableLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/blastTable.tsv',
+            locationType: 'UriLocation',
+        },
+    },
+    columns: {
+        type: 'string',
+        description: 'Optional space-separated column name list. If custom columns were used in outfmt, enter them here exactly as specified in the command. At least qseqid, sseqid, qstart, qend, sstart, and send are required',
+        defaultValue: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore',
+    },
+}, { explicitlyTyped: true });
+exports.default = BlastTabularAdapter;

package/dist/BlastTabularAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function BlastTabularAdapterF(pluginManager: PluginManager): void;

package/dist/BlastTabularAdapter/index.js

@@ -0,0 +1,42 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BlastTabularAdapterF;
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function BlastTabularAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'BlastTabularAdapter',
+        displayName: 'Tabular BLAST output adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BlastTabularAdapter'))).then(r => r.default),
+    }));
+}

package/dist/ChainAdapter/ChainAdapter.d.ts

@@ -1,5 +1,5 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class ChainAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         qname: string;

package/dist/ChainAdapter/ChainAdapter.js

@@ -3,17 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-// locals
-const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
+const io_1 = require("@jbrowse/core/util/io");
 const util_2 = require("./util");
+const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class ChainAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('chainLocation'), this.pluginManager);
-        const buffer = (await loc.readFile(opts));
-        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         return (0, util_2.paf_chain2paf)(buf);
     }
 }

package/dist/ChainAdapter/configSchema.d.ts

@@ -1,33 +1,19 @@
 declare const ChainAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     chainLocation: {
         type: string;
         defaultValue: {

package/dist/ChainAdapter/configSchema.js

@@ -1,41 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config ChainAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ChainAdapter = (0, configuration_1.ConfigurationSchema)('ChainAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the target assembly',
     },
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the query assembly',
     },
-    /**
-     * #slot
-     */
     chainLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },

package/dist/ChainAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ChainAdapterF(pluginManager: PluginManager): void;

package/dist/ChainAdapter/util.js

@@ -1,31 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_chain2paf = paf_chain2paf;
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
-/* adapted from chain2paf by Andrea Guarracino, license reproduced below
- *
- * MIT License
- *
- * Copyright (c) 2021 Andrea Guarracino
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
 function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
     return {
         qname,
@@ -56,34 +31,21 @@ function paf_chain2paf(buffer) {
     let cigar = '';
     const records = [];
     let blockStart = 0;
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const l = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        const l = decoder.decode(b).trim();
         blockStart = n + 1;
-        const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
+        const l_tab = l.replaceAll(' ', '\t');
         const l_vec = l_tab.split('\t');
         if (l_vec[0] === 'chain') {
-            // Emit previous PAF row, if available
             if (cigar) {
                 records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
             }
-            // Save query/target information
-            // score -- chain score
-            // tName -- chromosome (reference sequence)
-            // tSize -- chromosome size (reference sequence)
-            // tStrand -- strand (reference sequence)
-            // tStart -- alignment start position (reference sequence)
-            // tEnd -- alignment end position (reference sequence)
-            // qName -- chromosome (query sequence)
-            // qSize -- chromosome size (query sequence)
-            // qStrand -- strand (query sequence)
-            // qStart -- alignment start position (query sequence)
-            // qEnd -- alignment end position (query sequence)
-            // id -- chain ID
             t_name = l_vec[2];
             t_start = +l_vec[5];
             t_end = +l_vec[6];
@@ -97,18 +59,10 @@ function paf_chain2paf(buffer) {
                 q_start = +q_size - q_end;
                 q_end = +q_size - tmp;
             }
-            // Initialize PAF fields
             num_matches = 0;
             cigar = '';
         }
         else {
-            // size -- the size of the ungapped alignment
-            //
-            // dt -- the difference between the end of this block and the beginning
-            //    of the next block (reference sequence)
-            //
-            // dq -- the difference between the end of this block and the beginning
-            //    of the next block (query sequence)
             const size_ungapped_alignment = +l_vec[0] || 0;
             const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
@@ -124,7 +78,6 @@ function paf_chain2paf(buffer) {
             }
         }
     }
-    // Emit last PAF row, if available
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }

package/dist/DeltaAdapter/DeltaAdapter.d.ts

@@ -1,5 +1,5 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         qname: string;

package/dist/DeltaAdapter/DeltaAdapter.js

@@ -3,17 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const io_1 = require("@jbrowse/core/util/io");
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("@jbrowse/core/util");
-// locals
-const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
+const io_1 = require("@jbrowse/core/util/io");
 const util_2 = require("./util");
+const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class DeltaAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager);
-        const buffer = (await loc.readFile(opts));
-        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         return (0, util_2.paf_delta2paf)(buf);
     }
 }

package/dist/DeltaAdapter/configSchema.d.ts

@@ -1,33 +1,19 @@
 declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: string;
         defaultValue: {